Tone controls are just another tool in the arsenal that is available to be used if you so desire.
You could use the built in tone controls of your amp and the Loki at the same time if you want to, but assuming that the built in tone controls are just a bass and treble adjustment and the Loki being only 4 bands you probably will not see much benefit in doing so.
If you were using a 1/3 octave e.q. to tune your system to your room and then use the Loki or your built in tone controls to adjust for variations in recordings you should see a more dramatic difference.
You could use the built in tone controls of your amp and the Loki at the same time if you want to, but assuming that the built in tone controls are just a bass and treble adjustment and the Loki being only 4 bands you probably will not see much benefit in doing so.
If you were using a 1/3 octave e.q. to tune your system to your room and then use the Loki or your built in tone controls to adjust for variations in recordings you should see a more dramatic difference.